Protocols - DNA Digest

DNA Digest

Description
The fragmentation of DNA using restriction endonucleases (REs).

Approx. Duration:

Preparation

~5 minutes

Setting up the digest

~10 minutes

Whole Protocol

~1 hour 15 minutes

Uses
Analysis of plasmid, cosmid or genomic DNA in combination with various methods, e.g. Southern Blots, cloning, checking mini preps. Visualisation is achieved by running the/a sample of the digest on a agarose gel.

Prerequisites
Ideally you should have access to the sequence of the DNA you wish to analyse, if not a map should suffice. This will help make sense of the restriction pattern when run on an agarose gel and/or isolating a specific fragment for sub-cloning.

Preparation
Thaw all the samples on ice, except the enzymes which are removed when needed. Label all tubes and ensure the incubator is ready.

Method
Add the ingredients in order, to a MCT and place in the incubator @ 37°C for 1 hour (3 hours - overnight for larger digests)

Total Volume - 20µL:

dH2O

16µL

Buffer

2µL

DNA

1µL

RE

1µL

Optional:

RNase

1µL

ALP

1µL

Example of a larger digest (volume of DNA depends on its concentration)

Total Volume - 200µL:

dH2O

173µL

Buffer

20µL

DNA

5µL

RE

2µL

Optional:

RNase

1µL

ALP

1µL

Notes
Remove the enzyme(s) from the freezer when needed and keep all the other ingredients on ice. Restriction enzymes are measured in units; 1 unit will completely digest 1µg of λDNA in 1 hour, under optimal conditions. Double digests are possible but you will need to consult the manufacturers documentation on which buffer is most compatible for both enzymes. The addition of RNase might be considered if a small DNA fragment is expected that the RNA may otherwise obscure. Alkaline Phosphatase is used when a fragment is cut from a plasmid/cosmid to prevent the DNA from re-ligating; the phosphate group on the 5' end is removed to prevent this. Another method to prevent re-ligation is to heat the MCT post-digest to 65°C for 3 minutes then transfer to ice.